Viral diseases cause major economic losses to the shrimp industry, including diseases caused by white spot syndrome virus (WSSV), infectious hypodermal and hematopoietic necrosis virus (IHHNV; renamed Decapod penstylhamaparvovirus 1), among others.
Endogenous virus elements (EVE) of IHHNV and WSSV have been reported. The IHHNV genome (AF218266.2; 3,909-bp) is integrated in various chromosomes of P. monodon genome from China (PM-nanhai2-001_Lachesis_group23__306, JACBPZ010000025.1) and P. monodon from Thailand (JABERT010000007.1) both 95-97% identical. Fragments of AF218266.2 are also present in two genomes of P. vannamei farmed in China [(QCYY01000759.1, Penaeus vannamei breed Kehai No.1 LVANscaffold_759, nucleotides 87-1851 and 936-2058, 95-96% identity) and P. vannamei isolate Guihai-1-2017-001_HiC_scaffold_2, JANIEY010000002.1, nucleotides 1294-2575, 68% identity).
Three IHHNV sequences have been reported from P. vannamei of Ecuador [(AY362548.1) 3,775-bp), (OL598344.2) 3,203-bp, and (OM728642.1) 3,902-bp] and portions of these genomes are also integrated in the genomes of P. monodon from Thailand (GCA_015228065.1, isolate SGIC_2016 chromosome 7) and P. vannamei from China (GCA_003789085.1, breed Kehai No.1 LVANscaffold_759). IHHNV isolates from Peru (like OM728641 4,122-bp) are also integrated in P. monodon chromosomes 7 and 35, the number of fragments varying per chromosome, 10 and 51, respectively. Results suggested that the currently farmed P. vannamei lines in Ecuador are tolerant to circulating IHHNV genotypes, prompting the industry to request delisting of IHHN disease by the World Organization for Animal Health (WHOA).
Delisting of IHHN disease should be addressed carefully because of the interaction of IHHNV-EVE with a transposable element (RTE-2_PMon, (3,656-bp) from P. monodon from Thailand that contains fragments of microsatellite markers similar to RTE-2_PMon, with potential for re-emerging of IHHNV via horizontal gene transfer. Around 200 members of this family show only 0.5-2% sequence divergency to the RTE-2_PMon consensus sequence, indicating its current translocation activity. We should wait until a new genome sequence for P. vannamei is available to determine the integration sites and evolution of IHHNV-EVEs, and their association with Simple Sequence Repeats (SSRs) and noncoding RNA potentially associated with slow growth and disease resistance/tolerance.